Review History


All reviews of published articles are made public. This includes manuscript files, peer review comments, author rebuttals and revised materials. Note: This was optional for articles submitted before 13 February 2023.

Peer reviewers are encouraged (but not required) to provide their names to the authors when submitting their peer review. If they agree to provide their name, then their personal profile page will reflect a public acknowledgment that they performed a review (even if the article is rejected). If the article is accepted, then reviewers who provided their name will be associated with the article itself.

View examples of open peer review.

Summary

  • The initial submission of this article was received on May 24th, 2021 and was peer-reviewed by 2 reviewers and the Academic Editor.
  • The Academic Editor made their initial decision on June 30th, 2021.
  • The first revision was submitted on July 7th, 2021 and was reviewed by 1 reviewer and the Academic Editor.
  • A further revision was submitted on July 27th, 2021 and was reviewed by the Academic Editor.
  • The article was Accepted by the Academic Editor on August 5th, 2021.

Version 0.3 (accepted)

· Aug 5, 2021 · Academic Editor

Accept

Dear Drs. Yang and colleagues:

Thanks for revising your manuscript based on the concerns raised by the reviewer. I now believe that your manuscript is suitable for publication. Congratulations! I look forward to seeing this work in print, and I anticipate it being an important resource for groups studying fall armyworm and insect pest management. Thanks again for choosing PeerJ to publish such important work.

Best,

-joe

[# PeerJ Staff Note - this decision was reviewed and approved by Jennifer Vonk, a PeerJ Section Editor covering this Section #]

Version 0.2

· Jul 20, 2021 · Academic Editor

Minor Revisions

Dear Drs. Yang and colleagues:

Thanks for revising your manuscript. The reviewers are very satisfied with your revision (as am I). Great! However, there are a few minor things to address. Please address these ASAP so we may move towards acceptance of your work.

Best,

-joe

·

Basic reporting

No comment.

Experimental design

No comment.

Validity of the findings

No comment.

Additional comments

The authors have revised the manuscript according to the reviewer's suggestions and answered or explained the questions one by one. I’m satisfied with these revisions they have made. There are a few minor points that still need some attention in References. Please correct them.

1. The full-name of PNAS should be used as “Proceedings of the National Academy of Sciences of the United States of America”.
2. The “of” should not be capitalized the first letter in “Journal of Integrative Agriculture”.
3. Wu Q, Jiang Y, and Wu K. 2019. Analysis of migration routes of the fall armyworm Spodoptera frugiperda (J. E. Smith) from Myanmar to China. Plant Protection 45:1-6, 18.

Version 0.1 (original submission)

· Jun 30, 2021 · Academic Editor

Major Revisions

Dear Drs. Yang and colleagues:

Thanks for submitting your manuscript to PeerJ. I have now received two independent reviews of your work, and as you will see, the reviewers raised some concerns about the research. Despite this, this the reviewers are optimistic about your work and the potential impact it will have on research studying fall armyworm and insect pest management. Thus, I encourage you to revise your manuscript, accordingly, taking into account all of the concerns raised by both reviewers.

While the concerns of the reviewers are relatively minor, this is a major revision to ensure that the original reviewers have a chance to evaluate your responses to their concerns.

Importantly, please ensure your Materials and Methods are clearly stated. The methods should be clear, concise and repeatable. Please ensure this, and make sure all relevant information and references are provided (especially for tools and databases used).

There are many minor suggestions to improve the manuscript (typos, nuances, etc.).

I agree with many of the concerns of the reviewers, and thus feel that their suggestions should be adequately addressed before moving forward.

I look forward to seeing your revision, and thanks again for submitting your work to PeerJ.

Good luck with your revision,

-joe

·

Basic reporting

No comment.

Experimental design

No comment.

Validity of the findings

No comment.

Additional comments

As we all know that fall armyworm (FAW), Spodoptera frugiperda (J. E. Smith), is one of the most destructive agricultural pests worldwide. FAW has quickly invaded the Yunnan Province, southern China in December 2018 and causes huge economic losses to agriculture production. It has been classified as the top first destructive pest in China because of the gluttony, strong migration ability and high fertility of FAW. In the past several years, plenty of researches were focused on the toxicity of insecticides to this pest, the monitoring of population dynamic and insecticide resistance, and control strategies in the field in China, but little information of full-length transcriptome analysis of FAW revealed novel detoxification genes.

In this study, the authors used PacBio single-molecule real-time (SMRT) sequencing to obtain the full-length transcriptome profile of FAW larval brain. They found that a total of 18,642 high-quality transcripts were observed with an average read length of 2371 bp, and 11,230 of which were successfully annotated in six public databases. Among these, 5692 alternative splicing events were identified. In addition, five main gene families associated with the detoxification function were classified, and they were 84 transcripts of cytochrome P450s including CYP4, CYP6, CYP9, and CYP12 clades, 54 transcripts of ATP-binding cassettes as A, B, E, F and G groups, 46 transcripts of carboxylesterases including A, B and C families, 33 transcripts of glutathione S-transferases from “Delta and Epsilon”, “Sigma” and “Omega”clades, and 31 transcripts of UDP-glucuronosyl transferases including 1 and 2 families. The methods and the results used in this study are scientifically sound. Their findings will greatly contribute to revealing the resistance mechanisms and further benefit the investigation of gene functions. However, this manuscript has few of errors as details in the lists of major and minor concerns as currently written. So I don’t think this manuscript is suitable for publication at present.

There are some deficiencies as illustrated in the following:
Major concerns:
1. As well-known that the detoxification sites are usually located in the midgut, fatbody and Malpighian tubules of insect, but not in the brain. Please explain why you select this tissue to analyze its transcriptome for revealing novel detoxification genes?
2. In Introduction (Page 3 Line 48), the reference described by “Wang et al. 2021” is not appropriate because it is not the original reference. Thus, I suggest the authors changed it into “Wu et al. 2019; Sun et al. 2021” following as:
Wu Q, Jiang Y and Wu K. 2019. Analysis of migration routes of the fall armyworm Spodoptera frugiperda (J. E. Smith) from Myanmar to China. Plant Protection 45:1-6.
Sun X-x, Hu C-x, Jia H-r, Wu Q-l, Shen X-j, Zhao S-y, Jiang Y-y, and Wu K-m. 2021. Case study on the first immigration of fall armyworm, Spodoptera frugiperda invading into China. Journal of Integrative Agriculture 20:664-672.

Minor Concerns:
1. In Abstract (Page 2 Line 37), the second “to” should be deleted.
2. In Page 4 Line 96, “14L:10D” should be changed into “14 h:10 h (L:D)”.
3. In Page 5 Lines 119 and 120, a space should be inserted in front of “1” and “0.9”, respectively. The same problem in Page 6 Lines 127 and 130 should be revised.
4. In Page 6 Line 142, please add developer information of “FigTree v1.4.3 software”.
5. In Figure 1 A, the Latin names of insect species shoule be in italics.

Recommendation:
I recommend the authors to further conduct the manuscript with Minor Revisions.

Reviewer 2 ·

Basic reporting

Yang et al has carried out an interesting study to sequence the full-length transcriptome of the major insect pest, the fall armyworm (Spodoptera frugiperda). Through their methods they convincingly identify detoxification genes, although no discussion is given about their novelty. This manuscript utilizes modern fourth-generation long read sequencing to capture full length transcripts and I believe it will be of general interest to the PeerJ readership.

Concerns are as follows:
Title: I am not sure what context “novel” is being used in. I may have missed it (and I apologize if I did), but don’t recall new genes being identified.
Introduction: I suggest the authors separate detoxification enzymes into their metabolic phases in paragraph three. A naïve reader may assume they have similar functions. Enzymes are also listed from line 80 without order.
Line 109: I assume you mean DNA contamination? It would be worth specifying what kind of contamination you sought to identify.
Line 128: rephrase “hmmscan procedure” to include mention of the tool HMMER (if this is what was used) and cite the tool that was used.
Line 152: It would be useful to redefine FAW here as you are starting a new section.
Line 153: Can remove “as the results showed” and simply state the results.
Line 154: Specify the criteria used to determine “full length,” although the reader can guess how this was done (identifying poly-A tails), it is worth guiding the reader along a little more.
Line 155: This sentence is difficult to parse.
Line 160: “comprehensively” is a bit strong of a word to use, suggest softening or removing.
Line 162: should be “Swiss-Prot”
Line 164: Not exactly sure what “the homology distribution of these transcripts was revealed” means. I can take a guess that the authors are referring to the results in Figure 1A where the species designation of the closest BLAST hit for each transcript is plotted? The reasoning behind this analysis is not exactly clear. Why was this carried out?
Line 167: why were “6,715” classified? was this all the genes that had go terms annotated or a subset? From the wording of the sentence if seems as though this is a subset, but I don’t think that is the case.
Line 183: should be “A phylogenetic” rather than “The phylogenetic”


Discussion: The authors seem to make connections between detoxification enzymes based on their discovery dates. I believe it would serve the reader and the paper to have comparisons framed in terms of metabolic phase. This would help to highlight how dissimilar the mechanisms of these enzymes are and why it is important to have good gene models for each of them when it comes to understanding resistance mechanisms.
Line 254-5: “ABCs … act in neutralizing the toxicity of pesticides and metabolites.” Interpretation of this sentence is somewhat true, although misleading. ABCs are a part of the tertiary metabolism and primarily function as transporters, they do not actively “neutralize” substrates. In direct contrast to this statement, ABCC2 is largely responsible for transport of activated Cry toxins into the cell, resulting in cell death. Insecticide resistance is derived from loss of function in ABCC2.
Line 261: “screened out” implies they were removed.
Line 291: ABCs and UGTs are highly dissimilar. ABCs are involved in transport across the cell membrane (phase 3 metabolism) and UGTs conjugate UDP-GA to metabolites to decrease hydrophobicity (phase 2 metabolism).
Figure 1A: The 'species unknown' and S. litura colours are identical.

Experimental design

I see no major problems with the methodology underlying the manuscript, however the expression is severely lacking in the results (it was quite difficult to parse some sentences). Furthermore, I also ask the authors go through the manuscript, especially in the methods, to make sure tools are being cited as I noticed multiple chunks without proper citations or versions (eg. Databases used).

Validity of the findings

no comment

All text and materials provided via this peer-review history page are made available under a Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.